Questions tagged [small-molecules]

A small molecule is a non-polymeric molecule, such as a cofactor or metabolite

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From SMILE get Amber force in Python

I have a list of SMILES of small molecules and I want to be able to simulate these molecules with an Amber force field in Python. Currently, I use RDkit to convert the smile into a PDB file: ...
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How can I identify acceptor and donor atoms using BioPython?

I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy). How can I identify donor and acceptor atoms in a chain?
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Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?

I found that Lipinski's rule of five states that Log P (octanol-water partition coefficient, lipophilicity measure) usually should not exceed 5. Many papers about drug discovery machine learning ...
Slowpoke's user avatar
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Building small molecules de novo

Can anyone recommend a protocol for building the 3D structure of a small molecule de novo, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, ...
Sevy's user avatar
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How do I convert an Excel file (.xlsx) to an .smi file format?

How do I convert an Excel file(.xlsx) to .smi file format? The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
Shahbaaz's user avatar